[Mne_analysis] Plotting topographies for MEG sensors

Fri Nov 2 05:53:13 EDT 2012

hi Diana,

can you confirm that this example renders properly on your machine?

http://martinos.org/mne/auto_examples/plot_topography.html#example-plot-topography-py

if yes, please send me the evoked fif file so I can investigate.

Best,
Alex

On Fri, Nov 2, 2012 at 1:25 AM, Diana Omigie <d.omigie at gmail.com> wrote:
> Thanks,
> I'm using neuromag. Comparing the evoked/raw channel names with layout
> names, I notice there is a space in the latter that isn't there in the
> former
>
> MEG 0113
> vs
> MEG0113
>
> Diana
>
>
> p.s.
> my script below
>
> #mne
> #export PATH=/home/do232950/MyPython/epd_free-7.2-2-rh5-x86_64/bin:$PATH
> #export PYTHONPATH=/home/do232950/MyPython/mne-python:$PYTHONPATH
> print __doc__
> #ipython
> import os
>
> import mne
> import pylab as pl
> import numpy as np
> from mne import fiff
> from mne.layouts import Layout
> from mne.viz import plot_evoked,plot_topo
> #conditions = ['Pa_Ac','Vav','A']
> conditions = ['A']
>
>
> #evoked=dict()
> #subj_id = ['s02']
> subj_id =
> ['s01','s02','s04','s05','s06','s07','s09','s10','s11','s12','s13','s14','s16','s17']
>
>
> for s, subj in enumerate(subj_id):
>  data_ave_path =  'Desktop/ave/'
>  for i, cond in enumerate(conditions):
>   fname= data_ave_path + subj + '/'+subj +'_'+ cond +'_ave.fif'
>   evoked= fiff.read_evoked(fname, setno=0, baseline=(None, 0))
>   layout=Layout('Vectorview-all',path='Desktop')
>  plot_topo(evoked, layout)
>  title="mne"
>  pl.figtext(0.03,0.93,title,color='w',fontsize=18)
>  pl.show()
>
>
>
>
> On Thu, Nov 1, 2012 at 6:55 PM, Denis-Alexander Engemann
> <d.engemann at fz-juelich.de> wrote:
>>
>> Hi Diana,
>>
>> could you share the script you were using?
>> Did you make sure that you were using the correct layout. In case your
>> MEG-system isn't a Neuromag 'vectorview-all' will not work. The plotting
>> function assumes that channel names of raw match the layout names.
>> So you could compare raw.ch_names with layout.names.
>>
>> Hope this helps.
>>
>> Denis
>>
>>
>>
>> On Thu, Nov 1, 2012 at 11:20 PM, Diana Omigie <d.omigie at gmail.com> wrote:
>>>
>>> Thanks both, unfortunately Im now getting the black image box with my
>>> title but no actual plots when I use the plot_topo function even though I
>>> can see the evoked object when I use plot_evoked.
>>>
>>> Diana
>>>
>>>
>>> On Thu, Nov 1, 2012 at 5:33 PM, Denis A. Engemann
>>> <denis.engemann at gmail.com> wrote:
>>>>
>>>> Hi Diana,
>>>>
>>>> this looks like the mne-python interface. Which version do you currently
>>>> use?
>>>> Recently there was an API change recently. Here is a script that
>>>> demonstrates how to do it with the current developmental version.
>>>>
>>>>
>>>> https://github.com/mne-tools/mne-python/blob/master/examples/time_frequency/plot_tfr_topography.py
>>>>
>>>>
>>>> Denis
>>>>
>>>>
>>>> On 01.11.2012, at 22:11, Diana Omigie <d.omigie at gmail.com> wrote:
>>>>
>>>> I am trying to plot meg evoked data using vector-view layouts but keep
>>>> getting the error message that the .lout files cannot be found when I call
>>>> this line
>>>>
>>>> layout = Layout('Vectorview-all')
>>>>
>>>> Any obvious reasons why I might be having trouble?
>>>>
>>>> Many thanks
>>>>
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